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NM_001034853.2(RPGR):c.3096_3097del (p.Glu1033fs) AND Retinitis pigmentosa 3

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Apr 8, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001251568.10

Allele description [Variation Report for NM_001034853.2(RPGR):c.3096_3097del (p.Glu1033fs)]

NM_001034853.2(RPGR):c.3096_3097del (p.Glu1033fs)

Gene:
RPGR:retinitis pigmentosa GTPase regulator [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
Xp11.4
Genomic location:
Preferred name:
NM_001034853.2(RPGR):c.3096_3097del (p.Glu1033fs)
Other names:
NM_001034853.2(RPGR):c.3096_3097del; p.Glu1033fs
HGVS:
  • NC_000023.11:g.38285905_38285906del
  • NG_009553.1:g.46633_46634del
  • NM_000328.3:c.1905+1191_1905+1192del
  • NM_001034853.2:c.3096_3097delMANE SELECT
  • NM_001367245.1:c.1902+1191_1902+1192del
  • NM_001367246.1:c.1719+1191_1719+1192del
  • NM_001367247.1:c.1572+5056_1572+5057del
  • NM_001367248.1:c.1602+5056_1602+5057del
  • NM_001367249.1:c.1569+5056_1569+5057del
  • NM_001367250.1:c.1569+5056_1569+5057del
  • NM_001367251.1:c.1386+5056_1386+5057del
  • NP_001030025.1:p.Glu1033fs
  • NC_000023.10:g.38145155_38145156del
  • NC_000023.10:g.38145158_38145159del
  • NM_001034853.1:c.3096_3097del
  • NM_001034853.1:c.3096_3097delGG
Note:
NCBI staff reviewed the sequence information reported in PubMed 11857109 Fig. 1a to determine the location of this allele on the current reference sequence.
Protein change:
E1033fs
Links:
OMIM: 312610.0014; dbSNP: rs606231180
NCBI 1000 Genomes Browser:
rs606231180
Molecular consequence:
  • NM_001034853.2:c.3096_3097del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000328.3:c.1905+1191_1905+1192del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367245.1:c.1902+1191_1902+1192del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367246.1:c.1719+1191_1719+1192del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367247.1:c.1572+5056_1572+5057del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367248.1:c.1602+5056_1602+5057del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367249.1:c.1569+5056_1569+5057del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367250.1:c.1569+5056_1569+5057del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001367251.1:c.1386+5056_1386+5057del - intron variant - [Sequence Ontology: SO:0001627]
Functional consequence:
protein truncation [Variation Ontology: 0015]

Condition(s)

Name:
Retinitis pigmentosa 3
Synonyms:
Cone-rod degeneration X-linked; Choroidoretinal degeneration with retinal reflex in heterozygous women; Retinitis pigmentosa 15
Identifiers:
MONDO: MONDO:0010227; MedGen: C1845667; Orphanet: 791; OMIM: 300029

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001427348Blueprint Genetics
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001573285Ocular Genomics Institute, Massachusetts Eye and Ear
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Apr 8, 2021) 		germlineresearch

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch, clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Blueprint Genetics, SCV001427348.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Ocular Genomics Institute, Massachusetts Eye and Ear, SCV001573285.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)

Description

The RPGR c.3096_3097del variant was identified in an individual with retinitis pigmentosa with a presumed X-linked inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PS1, PM2. Based on this evidence we have classified this variant as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 15, 2024